


the pegasus galaxy

by underworld_kings18



Series: What If...? [1]
Category: Stargate Atlantis
Genre: Alternate Universe - Canon Divergence, City of the Ancients, Gen, Post-Traumatic Stress Disorder - PTSD, angels are sorta known, but this is au so i'm winging it, he's also a cia agent, john sheppard has ptsd, probably episode compliant most of the time, rodney mckay is an archangel of the lord
Language: English
Status: In-Progress
Published: 2021-01-17
Updated: 2021-01-17
Packaged: 2021-03-15 17:23:07
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 2
Words: 2,090
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/28817028
Author URL: https://archiveofourown.org/users/underworld_kings18/pseuds/underworld_kings18
Summary: in this reality, elizabeth weir is a little bit more prepared to send a hundred people to another galaxy. unfortunately, that doesn't mean all of her people are stable, in a sense. in this reality john sheppard is a hero who has lost everything he loved. in this reality, rodney mckay is an angry, broken ex-angel and cia spy. in this reality, some of the decisions are made better, and some situations go much, much worse.billions of lightyears from their home, elizabeth weir is in charge of 98 men and women, they're living in the Lost City of Atlantis, and they truly had no idea just what they were getting themselves into
Series: What If...? [1]
Series URL: https://archiveofourown.org/series/2112801
Kudos: 4





	1. Chapter 1

**Author's Note:**

> welcome to my revised Stargate Atlantis series. I'm hoping this will stick as close to Canon as i can get it, but as i am adding the existence of angels and demons, not to mention spicing up Rodney's background and Sheppard's mental health because as a writer i can do that
> 
> this is in no way an insult to the original series, which is absolutely fantastic and i am re-watching for the 11th time. but i do believe they went into this expedition woefully unprepared.
> 
> the updates likely will not be consistent to start with. i have up to leaving on the expedition written, including some info on rodney's cia days, as well as a little insight to the 'fallen 7' which will be important later in the series, but i haven't even started with the first few episodes.
> 
> cast list will be at the end of the chapter

**1\. The preparations are made for the atlantis expedition, taking into consideration staffing, budgets, and the gene. then jack o'neill somehow finds an air force major in self-exile with the gene in spades**

The preparation for the Atlantis mission took from December 2003 to June 2004. The first week Elizabeth spent writing up lists and then tearing them up. The second week she spoke with doctor lam and a quartermaster on base, who outlined what she may potentially need on the expedition, and then she spoke to the botany department to enquire about plants they could bring, animals at a stretch. After that enlightening conversation she located General O’Neill and the two of them sat down.

“Look, General, we’re launching an expedition to another galaxy, where the potential of us being cut off from Earth are very high.” Elizabeth explained. “My budget is not large enough. In fact, the money here barely covers the medical supplies we will need to take. Fact is, General, that this mission could very well be one way, and we need every possible advantage if we’re going to survive.” Jack sighed, leaning back in his chair, silently cursing the IOA. He knew the budget was going to be a problem.

“Yeah, I thought as much. Get me the lists by the end of the month, i'll make sure you get everything you need."

After Elizabeth, Doctor Rodney McKay was the first person to sign onto the expedition officially, followed by Doctor Carson Beckett, Doctor Radek Zelenka, Colonel Marshall Sumner and lastly Lieutenant Aiden Ford, which rounded out her senior staff. The IOA had given them a max personnel limit of a hundred, including themselves, and Lam gave them a list of the gene carriers they had within the various programs the SGC had and the adjacent projects. Since it was a mostly scientific exploration mission, Sumner agreed that they likely would only need 30 military officers, meaning that the last 70 would need to be divided up equally between Medical and the different scientific fields. And Elizabeth sat down with Doctor Jackson and both of them decided on what would be needed to start a colony on another world.

In March 2004, most of the personnel had been selected and all of them had accepted, mostly due to their gene, Elizabeth, Rodney and Carson were spending most of their time at the Ancient Outpost, which is how they met Major John Sheppard, who's gene was as strong as General O'Neill's was.

**antarctica...  
  
**

Major John Patrick Sheppard was tired. He wasn’t entirely sure when it started, but he noticed it when he got after Afghanistan and then he took an assignment at McMurdo Base in Antarctica, assigned as a glorified taxi driver ferrying scientists and marines to an outpost in the middle of the Antarctic landscape. He knew it was more than it seemed, likely was more than just the dome that covered it, but it was classified and honestly, he didn't have the energy to ask questions he wouldn't get answers too.

He was also smart enough to realise he had a textbook case of depression, but he figured that was to be expected, what with carrying his best friend’s dead body 80 miles through the desert getting shot at by the Taliban after being shot out of the sky mere seconds before he was forced to make the choice between returning to base and disobeying a direct order. For it he was awarded the Air Force Cross medal, which had come as a surprise to John since he’d figured he’d get black marked or discharged.

So, for four months, his life was routine. He woke up, he tried to eat breakfast, though he usually gave up about half way through, not hungry, showered, then sat around reading the books he had while he awaited an assignment and skipping lunch, then had dinner, following the same routine as breakfast, and slept, plagued by nightmares of the accident. When he did get the chance to get off base, it was usually every other day either to ferry a new marine or scientist over to the base, or to pick somebody up from said base to return to the States. Every trip took 40 minutes round trip with his flying, faster than the other pilots, and it was all routine, at least until he met Major General Jack O’Neill, USAF. Then his life was never quite the same.

_“Apache, Blackhawk, Cobra, Osprey…”_ John replied. His answer felt forced, and he hated that. It wasn’t who he was, yet some days were a harder than others, and it was getting harder and harder to function daily. He was worried that one day, he might just stop answering all together.

_“It's a lot of training for the Antarctic.”_ Jack noted casually, glancing at the pilot. He wasn’t an idiot, he could see there was something wrong here. A man with Sheppard's record shouldn't sound like he was forcing himself to reply, just to function.

_“It was the one continent I never set foot on.”_ John shrugged.

_“It's one of my least favourite continents.”_ Jack grimaced, keeping the conversation light.

_“I kind of like it here.”_ John admitted.

_“You like it here?”_ Jack asked, voice an octave higher in disbelief.

_“Yes, sir. Be there in about ten minutes, sir.”_ Jack exhaled silently and sat back in his seat. He had a feeling it was going to be harder than just a conversation to figure out what was going on with the Pilot.

7 minutes later John was landing his Helicopter for the second time in the last 20 minutes, though this time at the proper destination, and this time without the potential threat of near death at the hands of a freaking glowing squid-looking missile trying to blow them out of the sky. He cut off the rotors and engines and just sort of, sat there, staring out the glass to the snowy landscape. Jack waited, knowing what was coming.

“What the hell was that?” John finally asked, pulling his helmet off and scrubbing a hand over his hair that was definitely not regulation cut - not that his own was either, since he was a bloody hero and nobody dared say a word about his hair. "It- it looked like a goddamn flying squid? What was with those, tentacle-looking things? I mean _what_?" He glanced back at the drone, which Jack had, albeit reluctantly, insisted they load up into the back of the helicopter to bring back to the outpost.

“We call them drones.” Jack answered, removing his own headset and hanging it up beside the seat. “You’ll need to sign an NDA when we get back to McMurdo. Major, this shit is ridiculously classified.” John looked at Jack, his expression blank. “Are you alright? I’ve had enough trauma to notice that you look one major incident away from eating your own gun.”

“Honestly, sir?” John asked. Jack nodded. “I feel kind of, numb. That’s why I asked for this assignment. 3 years and I can retire.”

“How much do you think you’ve got in ya?”

“That depends.” John said honestly.

“On?”

“If whatever’s thrown at me next is to big for me to handle.”

“Well, let’s find out shall we.” Jack climbed out of the helicopter and reluctantly John did the same, following the General into the Dome that covered the outpost. After sending directions to a couple of marines to collect the drone in the back of John's helicopter, the General directed them into enter an elevator, where there was a marine standing at the controls.

“General.” The marine greeted.

“Sergeant.” Jack nodded back. The gate shut behind them and the Sergeant started the lift, sending them down. “Coupla ground rules, Major. Don’t touch anything, don’t get in the way, and don’t tell anyone about this once you leave.”

“Yes sir.” John nodded. With his sunglasses off Jack could see just how exhausted the Major was, with dark bruises under his eyes, his face looked rather gaunt as well. Christ, he looked ready to collapse. Jack just hoped that all of this didn’t break the Major.


	2. Chapter 2

**Summary for the Chapter:**

> continuation...
> 
> season 1 episode 1&2 ; rising
> 
> jack and elizabeth talk about john sheppard, then jack has a frank and uncomfortable conversation with sheppard about his mental health, and john is introduced to the sgc

**Notes for the Chapter:**

> this is just a rough draft. if i get positive feedback, i'll likely upload edited and more in-depth chapters
> 
> rude comments will be deleted, constructive criticism is allowed but i reserve the right to hate it

**the ancient outpost...**

Jack was heading back towards the elevator, speaking with Doctor Weir as they went.

“We could be on our way to discovering an entirely new Ancient civilization. The best case scenario, we meet actual Ancients who are willing to help us, but if we don't…” Jack glanced at the stasis chamber he’d been stuck in for several months during his second brush with near death with one of those damn ancient head suckers. Waking up on Thor’s ship months later with a couple of extra changes left over had been an adjustment, to say the least. “General, we need him.”

“Sorry, Doc, I need Daniel here.”

“I'm talking about Major Sheppard.” Elizabeth said. She and Daniel could argue themselves hoarse in regard to Daniel joining the expedition, but there was no way Jack was letting him go unless he could come back.

“Oh. Don't you have a dozen or so people already who can use the Ancient technology?” Jack asked.

“Yes, with concentration and training, they can make it work, but John Sheppard, he does it naturally.”

“You know, I've checked into his record.” Jack said when they stopped just outside the elevator.

“Yes, an Air Force Cross. He was trying to save the lives of three servicemen and nearly lost his own in the process.”

“Indirectly disobeying a direct order in the process.”

“I have read your own file, General. Please.” Elizabeth said ironically. "And besides, his helicopter went down before he could recieve the re-call order."

“Right.” Jack sighed. “Okay, it's your expedition. You want him, you ask him.”

“Uh, that's the thing. I have.” She admitted.

“Really?” Jack asked in surprise. “Uh, by any chance did he just stand there, reply with one worded answers when he could run away like his ass was on fire?”

“Um, yes he did.”

“Crap.” Jack sighed. “I think the Major is displaying symptoms of depression, possibly PTSD. Related to the accident 8 months ago.” Elizabeth frowned, concerned.

“I know that look. What are you planning, Jack?”

“It’s probably better you don’t know.”

**cheyenne mountain, colorado...**

The next several days passed by so fast that John wasn’t entirely sure what was happening until he was sitting in General O’Neill’s office under Cheyenne Mountain, dressed in the official Atlantis Uniform, digesting the information that yes, aliens were real and yes, since 1998 the USAF have been sending people to other planets in the search for allies, technology and most recently, the Lost City of Atlantis. And yet somehow, none of it was shocking or too much to take in, as though he was destined to know this, to travel to another Galaxy.

“Before I send you on your way to sit in Doctor Zelenka’s lab and turn stuff on, I want to talk to you about something.” Jack said seriously.

“I don't know what you're talking about.” John replied instinctively, his tone just on the wrong side of tense. The General saw right through his bullshit.

“I want you to know we have several in-the-know therapists who can help you.” Jack said seriously. He looked wildly uncomfortable having this conversation, which soothed John a little knowing that General O’Neill was as uncomfortable as he was. “All this isn’t going to just, go away, trust me on that. We’re sending a therapist with the Expedition, a Doctor Kate Heightmeyer, I can set up an appointment with her, or someone else if you’d prefer.” John grimaced at the idea of speaking to a therapist.

“My Father would kill me if he found out.” John admitted warily. “And realistically, I shouldn’t care that someone who disowned me when I was 16 finding out but-”

“But you can’t help that. So he doesn’t find out.” Jack dismissed. “This project is so classified out therapists have to sign NDA’s with every patient. Doing it through us also keeps it off your Personal Insurance. Your Father will never know.”

“You think it might help?” John asked reluctantly.

“It helped me.” Jack shrugged. “Look Major, I can’t make you go. You’ll go on the Expedition whether you go to therapy or not. But best case is that talking about it helps you, and worst it doesn’t. It won’t hurt to go.” John nodded. He’d go, he’d try.

“I’ll try.”

“Great. Now go, before I have Carter on my ass because i’m holding up her light switch.”

"Yes sir."

**Notes for the Chapter:**

> ugh honestly i kind of hate it

**Author's Note:**

> authors note  
> this is part one of the first episode. likely it will be a fair few parts, but it won't be the entire episodes. just the parts where things are different from the show i guess
> 
> starring;
> 
> torri higginson as doctor elizabeth weir, leader of the expedition  
> joe flanigan as major john sheppard, military leader/2ic, ar-1  
> david hewlett as doctor rodney mckay, science leader, ar-1, raziel, ex-cia  
> rainbow sun franks as lieutenant aiden ford, ar-1  
> rachel luttrell as teyla emmagan, athosian leader, ar-1  
> david nykl as doctor radek zelenka, science 2IC, head engineer  
> scott eastwood as master gunnery sergeant robert stackhouse, quartermaster, ar-2  
> alexander skarsgard as corporal jordan stevens, ar-3  
> vaani kapoor as staff sergeant saarya walker, ar-2  
> paul mcgillion as doctor carson beckett, medical leader  
> dean marshall as sergeant eugene bates, head of security  
> dan payne as lieutenant daniel reed, security officer  
> ben cotton as doctor kavanagh, engineer
> 
> more added as the series goes on. they might not all have face claims if i can't find one suitable, so it will be a, imagine from description situation.
> 
> enjoyy


End file.
